6UL6 | pdb_00006ul6

Crystal Structure of BoNT/A-LCHn domain in complex with VNA ciA-D12/11/ciA-B5 and VHH ciA-H7

• PDB DOI: https://doi.org/10.2210/pdb6UL6/pdb

• Classification: TOXIN/ANTITOXIN
• Organism(s): Clostridium botulinum, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-07 Released: 2020-03-04 
• Deposition Author(s): Lam, K., Jin, R.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins

Lam, K., Tremblay, J.M., Vazquez-Cintron, E., Perry, K., Ondeck, C., Webb, R., McNutt, P.M., Shoemaker, C.B., Jin, R.

(2020) Cell Rep 30: 2526

• DOI: https://doi.org/10.1016/j.celrep.2020.01.107

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 141.99 kDa 
• Atom Count: 10,407 
• Modeled Residue Count: 1,208 
• Deposited Residue Count: 1,261 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BoNT/A	A	873	Clostridium botulinum	Mutation(s): 0  Gene Names: a, A, boNT, bonta, ACP52_06670 EC: 3.4.24.69
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore P0DPI1  Go to UniProtKB:  P0DPI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ciA-D12/11/ciA-B5	B	265	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ciA-H7	C	123	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.288	α = 90
b = 90.253	β = 119.037
c = 144.771	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Lam, K., Jin, R.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary